Research workbench
Crystal structure of fast switching M159T mutant of fluorescent protein dronpa (DRONPA2), Y63(3-iy)
Analyse Crystal structure of fast switching M159T mutant of fluorescent protein dronpa… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NQO
- Type
- protein
- Length
- 1,741 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fluorescent protein dronpa
- UniProt
- Q5TLG6
- Ligands
- KZG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 57% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Fluorescent protein dronpa | protein | 220 | 4% helix, 56% strand | Q5TLG6 |
| B, C, H | Fluorescent protein dronpa | protein | 216 | 4% helix, 57% strand | Q5TLG6 |
| D | Fluorescent protein dronpa | protein | 215 | 4% helix, 58% strand | Q5TLG6 |
| E | Fluorescent protein dronpa | protein | 218 | 4% helix, 57% strand | Q5TLG6 |
| G | Fluorescent protein dronpa | protein | 220 | 5% helix, 56% strand | Q5TLG6 |
Ligands and binding sites
- KZG · {(4Z)-2-[(1R)-1-amino-2-sulfanylethyl]-4-[(4-hydroxy-3-iodophenyl)methylidene]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 798 | 0.84 | 0.87 | 95 | empty |
| 2 | 100 | 0.78 | 0.98 | 25 | KZG |
| 3 | 99 | 0.77 | 0.98 | 28 | KZG |
| 4 | 90 | 0.77 | 0.98 | 25 | KZG |
| 5 | 95 | 0.76 | 0.98 | 26 | KZG |
Interfaces
16 interfaces between chains.
- A–B · 1341 Ų buried · 23 hydrogen bonds · protein-protein
- D–F · 1257 Ų buried · 19 hydrogen bonds · protein-protein
- C–E · 1244 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1243 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 865 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 covalent (covalent ligand).
Compared structures
- 6NQO · Crystal structure of fast switching M159T mutant of fluorescent protein Dronpa (Dronpa2)… · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q5TLG6
- Elsewhere: RCSB PDB 6NQO · PDBe 6NQO · UniProt Q5TLG6
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